def importFromDICOMWeb(dicomWebEndpoint, studyInstanceUID, seriesInstanceUID=None, accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Example usage:
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
"""
from dicomweb_client.api import DICOMwebClient
import random
if accessToken is None:
client = DICOMwebClient(url = dicomWebEndpoint)
else:
client = DICOMwebClient(
url = dicomWebEndpoint,
headers = { "Authorization": "Bearer {}".format(accessToken) },
)
seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if not seriesInstanceUID is None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
fileNumber = 0
for currentSeriesInstanceUID in seriesInstanceUIDs:
instances = client.retrieve_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime().toString("yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instance in instances:
filename = outputDirectoryPath + "/" + str(fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
slicer.app.processEvents()
importDicom(outputDirectoryPath)
return seriesInstanceUIDs
def _search_for_series(args):
'''Searches for Series and writes metadata to standard output.'''
params = _parse_search_parameters(args)
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
series = client.search_for_series(args.study_instance_uid, **params)
_print_metadata(series, args.prettify, args.dicomize)
def importFromDICOMWeb(dicomWebEndpoint,
studyInstanceUID,
seriesInstanceUID=None,
accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Progress is displayed and if errors occur then they are displayed in a popup window in the end.
If all the instances in a series are already imported then the series will not be retrieved and imported again.
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
Example: calling from PythonSlicer console
.. code-block:: python
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
"""
from dicomweb_client.api import DICOMwebClient
seriesImported = []
errors = []
clientLogger = logging.getLogger('dicomweb_client')
originalClientLogLevel = clientLogger.level
progressDialog = slicer.util.createProgressDialog(
parent=slicer.util.mainWindow(), value=0, maximum=100)
try:
progressDialog.labelText = f'Retrieving series list...'
slicer.app.processEvents()
if accessToken is None:
client = DICOMwebClient(url=dicomWebEndpoint)
else:
client = DICOMwebClient(
url=dicomWebEndpoint,
headers={"Authorization": f"Bearer {accessToken}"},
)
seriesList = client.search_for_series(
study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if seriesInstanceUID is not None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
# Turn off detailed logging, because it would slow down the file transfer
clientLogger.setLevel(logging.WARNING)
fileNumber = 0
cancelled = False
for seriesIndex, currentSeriesInstanceUID in enumerate(
seriesInstanceUIDs):
progressDialog.labelText = f'Retrieving series {seriesIndex+1} of {len(seriesInstanceUIDs)}...'
slicer.app.processEvents()
try:
seriesInfo = client.retrieve_series_metadata(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
numberOfInstances = len(seriesInfo)
# Skip retrieve and import of this series if it is already imported
alreadyImportedInstances = slicer.dicomDatabase.instancesForSeries(
currentSeriesInstanceUID)
seriesAlreadyImported = True
for serieInfo in seriesInfo:
sopInstanceUID = serieInfo['00080018']['Value'][0]
if sopInstanceUID not in alreadyImportedInstances:
seriesAlreadyImported = False
break
if seriesAlreadyImported:
seriesImported.append(currentSeriesInstanceUID)
continue
instances = client.iter_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime(
).toString("yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(
outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instanceIndex, instance in enumerate(instances):
progressDialog.setValue(
int(100 * instanceIndex / numberOfInstances))
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
filename = outputDirectoryPath + "/" + str(
fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
if cancelled:
# cancel was requested in instance retrieve loop,
# stop the entire import process
break
importDicom(outputDirectoryPath)
seriesImported.append(currentSeriesInstanceUID)
except Exception as e:
import traceback
errors.append(
f"Error importing series {currentSeriesInstanceUID}: {str(e)} ({traceback.format_exc()})"
)
except Exception as e:
import traceback
errors.append(f"{str(e)} ({traceback.format_exc()})")
finally:
progressDialog.close()
clientLogger.setLevel(originalClientLogLevel)
if errors:
slicer.util.errorDisplay(
f"Errors occurred during DICOMweb import of {len(errors)} series.",
detailedText="\n\n".join(errors))
elif cancelled and (len(seriesImported) < len(seriesInstanceUIDs)):
slicer.util.infoDisplay(
f"DICOMweb import has been interrupted after completing {len(seriesImported)} out of {len(seriesInstanceUIDs)} series."
)
return seriesImported
def importFromDICOMWeb(dicomWebEndpoint,
studyInstanceUID,
seriesInstanceUID=None,
accessToken=None):
"""
Downloads and imports DICOM series from a DICOMweb instance.
Example usage:
from DICOMLib import DICOMUtils
loadedUIDs = DICOMUtils.importFromDICOMWeb(dicomWebEndpoint="https://yourdicomweburl/dicomWebEndpoint",
studyInstanceUID="2.16.840.1.113669.632.20.1211.10000509338")
accessToken="YOUR_ACCESS_TOKEN")
:param dicomWebEndpoint: Endpoint URL for retrieving the study/series from DICOMweb
:param studyInstanceUID: UID for the study to be downloaded
:param seriesInstanceUID: UID for the series to be downloaded. If not specified, all series will be downloaded from the study
:param accessToken: Optional access token for the query
:return: List of imported study UIDs
"""
from dicomweb_client.api import DICOMwebClient
import random
progressDialog = slicer.util.createProgressDialog(
parent=slicer.util.mainWindow(), value=0, maximum=100)
progressDialog.labelText = f'Retrieving series list...'
slicer.app.processEvents()
if accessToken is None:
client = DICOMwebClient(url=dicomWebEndpoint,
callback=progressCallback)
else:
client = DICOMwebClient(
url=dicomWebEndpoint,
headers={"Authorization": f"Bearer {accessToken}"},
)
seriesList = client.search_for_series(study_instance_uid=studyInstanceUID)
seriesInstanceUIDs = []
if not seriesInstanceUID is None:
seriesInstanceUIDs = [seriesInstanceUID]
else:
for series in seriesList:
currentSeriesInstanceUID = series['0020000E']['Value'][0]
seriesInstanceUIDs.append(currentSeriesInstanceUID)
fileNumber = 0
cancelled = False
for seriesIndex, currentSeriesInstanceUID in enumerate(seriesInstanceUIDs):
progressDialog.labelText = f'Retrieving series {seriesIndex+1} of {len(seriesInstanceUIDs)}...'
slicer.app.processEvents()
instances = client.retrieve_series(
study_instance_uid=studyInstanceUID,
series_instance_uid=currentSeriesInstanceUID)
progressDialog.setValue(
int(100 * seriesIndex / len(seriesInstanceUIDs)))
slicer.app.processEvents()
cancelled = progressDialog.wasCanceled
if cancelled:
break
outputDirectoryBase = slicer.dicomDatabase.databaseDirectory + "/DICOMweb"
if not os.access(outputDirectoryBase, os.F_OK):
os.makedirs(outputDirectoryBase)
outputDirectoryBase += "/" + qt.QDateTime.currentDateTime().toString(
"yyyyMMdd-hhmmss")
outputDirectory = qt.QTemporaryDir(
outputDirectoryBase) # Add unique substring to directory
outputDirectory.setAutoRemove(False)
outputDirectoryPath = outputDirectory.path()
for instanceIndex, instance in enumerate(instances):
filename = outputDirectoryPath + "/" + str(fileNumber) + ".dcm"
instance.save_as(filename)
fileNumber += 1
importDicom(outputDirectoryPath)
if cancelled:
break
progressDialog.close()
return seriesInstanceUIDs
def get_files(self, ds, **kwargs):
print("Starting module LocalGetRefSeriesOperator")
if self.search_policy != 'reference_uid':
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print("Parameter 'modality' has to be set for search_policy: {} !".
format(self.search_policy))
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
client = DICOMwebClient(url=self.pacs_dcmweb,
qido_url_prefix="rs",
wado_url_prefix="rs",
stow_url_prefix="rs")
run_dir = os.path.join(WORKFLOW_DIR, kwargs['dag_run'].run_id)
batch_folder = [
f for f in glob.glob(os.path.join(run_dir, BATCH_NAME, '*'))
]
download_series_list = []
for batch_element_dir in batch_folder:
print("batch_element_dir: {}".format(batch_element_dir))
dcm_files = sorted(
glob.glob(os.path.join(batch_element_dir, "initial-input",
"*.dcm*"),
recursive=True))
if len(dcm_files) > 0:
incoming_dcm = pydicom.dcmread(dcm_files[0])
if self.search_policy == 'reference_uid':
if (0x0008, 0x1115) in incoming_dcm:
for ref_series in incoming_dcm[0x0008, 0x1115]:
if (0x0020, 0x000E) not in ref_series:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print(
"Could not extract SeriesUID from referenced DICOM series."
)
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
reference_series_uid = ref_series[0x0020,
0x000E].value
pacs_series = client.search_for_series(
search_filters={
'0020000E': reference_series_uid
})
if len(pacs_series) != 1:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print(
"Could not find referenced SeriesUID in the PACS: {} !"
.format(reference_series_uid))
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
download_series_list.append({
"reference_study_uid":
pacs_series[0]['0020000D']['Value'][0],
"reference_series_uid":
reference_series_uid,
"target_dir":
os.path.join(batch_element_dir,
self.operator_out_dir)
})
else:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print(
"Could not find referenced dcm-series within the metadata!"
)
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
if self.search_policy == 'study_uid':
pacs_series = client.search_for_series(
search_filters={
'0020000D': incoming_dcm.StudyInstanceUID,
'00080060': self.modality.upper()
})
if len(pacs_series) != 1:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print(
"Could not identify the searched modality: {} from the studyUID: {} !"
.format(self.modality,
incoming_dcm.StudyInstanceUID))
print(
"Number of possible DICOMs in the PACS: {}".format(
len(pacs_series)))
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
download_series_list.append({
"reference_study_uid":
pacs_series[0]['0020000D']['Value'][0],
"reference_series_uid":
pacs_series[0]['0020000E']['Value'][0],
"target_dir":
os.path.join(batch_element_dir, self.operator_out_dir)
})
if self.search_policy == 'patient_uid':
if not (0x0010, 0x0020) in incoming_dcm:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print(
"Could not extract PatientUID from referenced DICOM series."
)
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
patient_uid = incoming_dcm[0x0010, 0x0020].value
pacs_series = client.search_for_series(
search_filters={
'00100020': patient_uid,
'00080060': self.modality.upper()
})
if len(pacs_series) != 1:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print(
"Could not identify the searched modality: {} from the PatientUID: {} !"
.format(self.modality, patient_uid))
print(
"Number of possible DICOMs in the PACS: {}".format(
len(pacs_series)))
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
download_series_list.append({
"reference_study_uid":
pacs_series[0]['0020000D']['Value'][0],
"reference_series_uid":
pacs_series[0]['0020000E']['Value'][0],
"target_dir":
os.path.join(batch_element_dir, self.operator_out_dir)
})
if len(download_series_list) == 0:
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
print("")
print("No series to download could be found!")
print("Abort.")
print("")
print(
"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
)
exit(1)
for series in download_series_list:
print("Downloading series: {}".format(
series["reference_series_uid"]))
HelperDcmWeb.downloadSeries(
studyUID=series["reference_study_uid"],
seriesUID=series["reference_series_uid"],
target_dir=series['target_dir'])
def get_files(self, ds, **kwargs):
print("Starting module LocalGetRefSeriesOperator")
if self.search_policy != 'reference_uid' and self.modality is None:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print("Parameter 'modality' has to be set for search_policy: {} !".format(self.search_policy))
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
client = DICOMwebClient(url=self.pacs_dcmweb, qido_url_prefix="rs", wado_url_prefix="rs", stow_url_prefix="rs")
run_dir = os.path.join(WORKFLOW_DIR, kwargs['dag_run'].run_id)
batch_folder = [f for f in glob.glob(os.path.join(run_dir, BATCH_NAME, '*'))]
download_series_list = []
for batch_element_dir in batch_folder:
dcm_files = sorted(glob.glob(os.path.join(batch_element_dir, self.operator_in_dir, "*.dcm*"), recursive=True))
if len(dcm_files) > 0:
incoming_dcm = pydicom.dcmread(dcm_files[0])
if self.search_policy == 'reference_uid':
if (0x0008, 0x1115) in incoming_dcm:
for ref_series in incoming_dcm[0x0008, 0x1115]:
if (0x0020, 0x000E) not in ref_series:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print("Could not extract SeriesUID from referenced DICOM series.")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
reference_series_uid = ref_series[0x0020, 0x000E].value
pacs_series = client.search_for_series(search_filters={'0020000E': reference_series_uid})
print(f"Found series: {len(pacs_series)} for reference_series_uid: {reference_series_uid}")
if len(pacs_series) != 1:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print(f"Could not find referenced SeriesUID in the PACS: {reference_series_uid} !")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
download_series_list.append(
{
"reference_study_uid": pacs_series[0]['0020000D']['Value'][0],
"reference_series_uid": reference_series_uid,
"target_dir": os.path.join(batch_element_dir, self.operator_out_dir)
}
)
else:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print("Could not find referenced dcm-series within the metadata!")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
if self.search_policy == 'study_uid':
pacs_series = client.search_for_series(search_filters={'0020000D': incoming_dcm.StudyInstanceUID, '00080060': self.modality.upper()})
print(f"Found series: {len(pacs_series)} for modality {self.modality.upper()} in study: {incoming_dcm.StudyInstanceUID}")
if len(pacs_series) == 0 or (self.expected_file_count != "all" and len(pacs_series) != self.expected_file_count):
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print(f"Could not identify the searched modality: {self.modality} from the studyUID: {incoming_dcm.StudyInstanceUID} !")
print(f"Expected {self.expected_file_count} series of modality {self.modality} - found {len(pacs_series)} series")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
for series in pacs_series:
download_series_list.append(
{
"reference_study_uid": series['0020000D']['Value'][0],
"reference_series_uid": series['0020000E']['Value'][0],
"target_dir": os.path.join(batch_element_dir, self.operator_out_dir)
}
)
if self.search_policy == 'patient_uid':
if not (0x0010, 0x0020) in incoming_dcm:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print("Could not extract PatientUID from referenced DICOM series.")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
patient_uid = incoming_dcm[0x0010, 0x0020].value
pacs_series = client.search_for_series(search_filters={'00100020': patient_uid, '00080060': self.modality.upper()})
print(f"Found series: {len(pacs_series)} for modality {self.modality.upper()} in patient_uid: {patient_uid}")
if len(pacs_series) == 0 or (self.expected_file_count != "all" and len(pacs_series) != self.expected_file_count):
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print(f"Could not identify the searched modality: {self.modality} from the studyUID: {incoming_dcm.StudyInstanceUID} !")
print(f"Expected {self.expected_file_count} series of modality {self.modality} - found {len(pacs_series)} series")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
for series in pacs_series:
download_series_list.append(
{
"reference_study_uid": series['0020000D']['Value'][0],
"reference_series_uid": series['0020000E']['Value'][0],
"target_dir": os.path.join(batch_element_dir, self.operator_out_dir)
}
)
if len(download_series_list) == 0:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("")
print("No series to download could be found!")
print("Abort.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
exit(1)
results = ThreadPool(self.parallel_downloads).imap_unordered(self.download_series, download_series_list)
for result in results:
print(result)
